I don't know about anyone else, but I'd personally like to see a .pof constructor with the ability to create the hierarchy in that program (perferably WYSIWYG) rather than doing it beforehand in something like Truespace. By this I mean something like importing LOD 0 as the base, then importing totally seperate models (not necessarily restricted to .cob) in the "turret layer" (layers being akin to those used in Lightwave for example), the extra LOD's in their own layers, then link them through these layers into a final pof file. I've got this big mental 3D construct of what such a program would look like, don't know if these words quite get the idea across though.
Wouldn't it be easier to handle playing different mods with a -set game command, like in most FPS's? I know it would require modifying the source, but IMO that would be better than batch files and renaming folders etc.